One more strange thing is df doesn't show /nfs /nfs1 and /boot in its o/p, howevever mount -a complains those are mounted. Ofcourse those are, I checked if I see my data in mounted partitions, it's there.

no that is the correct path
just finished noting that you had all the options, was late seeing your config

# CONFIG_EXT2_FS is not set
# CONFIG_EXT3_FS is not set
CONFIG_EXT4_FS=y
CONFIG_EXT4_USE_FOR_EXT23=y
# CONFIG_EXT4_FS_POSIX_ACL is not set
# CONFIG_EXT4_FS_SECURITY is not set
# CONFIG_EXT4_DEBUG is not set

has been reported to help[, so has 'rootfstype=ext4' in the kernel line of grub.conf_________________Defund the FCC.

need to verify the fstype for
possible /dev line in /etc/fstab is devtmpfs (and not, for example, tmpfs)

the need for shm in fstab was eliminated with the inotify/dnotify kernel choices IIRC
check that /var/run is a symlink to /run
the /dev/root that appears in mount and df appoears to be anomalous; i don't have it_________________Defund the FCC.

mount: warning: /etc/mtab is not writable (e.g. read-only filesystem).
It's possible that information reported by mount(8) is not
up to date. For actual information about system mount points
check the /proc/mounts file.

No it wasn't completely new install. There is a story behind this one.

FYI. this was good working machine, with no such problems. With some crazy idea I decided to grow sda3 which is root file system, online. I changed END sectors(fdisk) for sda3 while system booted and ran resize2fs. That's when kernel crashed. Then booting with gparted I ran couple of fsck's which moved some data to lost+found. I didn't get anything back and lost all 40GB file system then. I recreated ext4 on it and rsynced everything over ssh while gparted was running from other working gentoo system. Omitted dev/ /mnt/ /sys..

I couldn't boot system with other system's lilo and its kernel, so I did install a newer kernel and recovered some things off of lost+found dir(via test disk image before ext4fs formatting). I had installed kernel in ch-rooted env which itself was pain for me to get it to work even with 64bit kernel sysrescue. I chrooted with /bin/tcsh shell which I am not familiar much. bash was failing due libtermcap.so I wonder why! This was one of the causes system didn't boot after kernel compilation but I had taken care of it before posting my issue here.

Anyway, I wonder why some services went missing for boot or default runlevel. I did come across a thread on gentoo forums where a user added 'root' to default to resolve similar problem.

In the end, I guess this was one of the things I had to check..

Just thought I'd post my rsync command. It's run from a good system running gentoo.